Protein Identification

Proteins are identified through the bottom-up proteomics scheme. Purified proteins or mixtures of proteins in solution or SDS-PAGE gels are digested with a protease, typically trypsin, and the proteolytic peptides are subjected to tandem mass spectrometry (MS/MS). The resulting MS/MS data are compared to protein databases via automated protein database searching to identify the proteins that contain the peptides detected by the mass spectrometer.

The higher the amount of protein available for use the higher the likelihood for successful identification; however, the identification of a single protein at 1-10 ng level is possible.

Sample Preparation

Sample preparation involves SDS-PAGE gel electrophoresis, digestion, and desalting of gel slices. Investigators can take their samples through the complete preparation, or the proteomics staff can assist with some steps. If you choose to prepare your own gel samples, see our Tips for SDS-PAGE Gel Handling

Sample Submission

If you are using a FHCRC project id for billing, please fill out the Internal Submission Form and submit with your sample.

If billing is to be submitted to the University of Washington or other external institution, fill out the External Submission Form and submit with your sample.

Analysis of Results

Data generated within the resource are transferred through automated pipelines to systems supported by the Hutchinson Center's Research Computing Support shared resource. Data can then be analyzed using the Computational Proteomics Analysis System (CPAS), a database repository and analysis tool developed at Fred Hutchinson. Information on how to use CPAS to analyze your results is available.

	Analysis of Results